南京林业大学学报(自然科学版)
南京林業大學學報(自然科學版)
남경임업대학학보(자연과학판)
JOURNAL OF NANJING FORESTRY UNIVERSITY(NATURAL SCIENCE EDITION)
2014年
2期
47-51
,共5页
孔凡明%王小龙%陈赢男%李淑娴%徐进%尹佟明
孔凡明%王小龍%陳贏男%李淑嫻%徐進%尹佟明
공범명%왕소룡%진영남%리숙한%서진%윤동명
表达序列标签%序列组装%微卫星%松属
錶達序列標籤%序列組裝%微衛星%鬆屬
표체서렬표첨%서렬조장%미위성%송속
expressed sequence tag%sequence assembly%microsatellites%pine
从GenBank下载453892条松属EST序列,序列组装后得到20886条contig。用Sputnik软件从这些contig中查找了2678个微卫星,其中3碱基重复微卫星占的比例最高,为59?2%,而其他重复长度的微卫星都相对较低,比例分别为:2碱基重复微卫星占12.0%,4碱基重复微卫星占13.3%,5碱基重复微卫星占15.5%。3碱基重复微卫星变化引起的基因读码框改变最小,松属树种基因区3碱基重复微卫星的富集显示了强烈的密码子选择效应。此次研究还对查找到的微卫星进行了引物设计和扩增分析。实验结果显示,设计的微卫星引物在云南松中的扩增成功率是72.9%。从扩增成功的引物中进一步选取了155对引物,对14个松属树种和1个黄杉属树种进行了引物通用性实验分析,结果显示155对引物在14个松属树种间的通用性在71.0%以上,而在黄杉属树种中的通用性只有25.2%。对松属树种中含有微卫星的基因进行了功能分类研究,结果显示基因在是否保留微卫星序列方面有显著分化,微卫星参与了如细胞成分分类的共质体组成、病毒颗粒及病毒颗粒组成、生物节律调控,以及生长素转运蛋白等生物学过程。
從GenBank下載453892條鬆屬EST序列,序列組裝後得到20886條contig。用Sputnik軟件從這些contig中查找瞭2678箇微衛星,其中3堿基重複微衛星佔的比例最高,為59?2%,而其他重複長度的微衛星都相對較低,比例分彆為:2堿基重複微衛星佔12.0%,4堿基重複微衛星佔13.3%,5堿基重複微衛星佔15.5%。3堿基重複微衛星變化引起的基因讀碼框改變最小,鬆屬樹種基因區3堿基重複微衛星的富集顯示瞭彊烈的密碼子選擇效應。此次研究還對查找到的微衛星進行瞭引物設計和擴增分析。實驗結果顯示,設計的微衛星引物在雲南鬆中的擴增成功率是72.9%。從擴增成功的引物中進一步選取瞭155對引物,對14箇鬆屬樹種和1箇黃杉屬樹種進行瞭引物通用性實驗分析,結果顯示155對引物在14箇鬆屬樹種間的通用性在71.0%以上,而在黃杉屬樹種中的通用性隻有25.2%。對鬆屬樹種中含有微衛星的基因進行瞭功能分類研究,結果顯示基因在是否保留微衛星序列方麵有顯著分化,微衛星參與瞭如細胞成分分類的共質體組成、病毒顆粒及病毒顆粒組成、生物節律調控,以及生長素轉運蛋白等生物學過程。
종GenBank하재453892조송속EST서렬,서렬조장후득도20886조contig。용Sputnik연건종저사contig중사조료2678개미위성,기중3감기중복미위성점적비례최고,위59?2%,이기타중복장도적미위성도상대교저,비례분별위:2감기중복미위성점12.0%,4감기중복미위성점13.3%,5감기중복미위성점15.5%。3감기중복미위성변화인기적기인독마광개변최소,송속수충기인구3감기중복미위성적부집현시료강렬적밀마자선택효응。차차연구환대사조도적미위성진행료인물설계화확증분석。실험결과현시,설계적미위성인물재운남송중적확증성공솔시72.9%。종확증성공적인물중진일보선취료155대인물,대14개송속수충화1개황삼속수충진행료인물통용성실험분석,결과현시155대인물재14개송속수충간적통용성재71.0%이상,이재황삼속수충중적통용성지유25.2%。대송속수충중함유미위성적기인진행료공능분류연구,결과현시기인재시부보류미위성서렬방면유현저분화,미위성삼여료여세포성분분류적공질체조성、병독과립급병독과립조성、생물절률조공,이급생장소전운단백등생물학과정。
In this study, 453 892 Pinus ESTs were downloaded from GenBank, and these ESTs were assembled into 20 886 contigs ( representing 20 886 unigenes of pines) with GS De novo assembler from roche, according to species, respectively. Searching by the Sputnik engine, 2 678 microsatellites were detected in the assembled contigs. It is noticea-ble that trinucleotide repeats were found to be the most abundant microsatellites in this database ( accounting for 59?2%) . By contrast, the richness of the other type of microsatellites were relatively low, with di-, tetra-, penta-nucleo-tide repeats accounted for 12.0%, 13.3% and 15.5% of the detected microsatellites, respectively. Dominance of triplet microsatellites in genes can be well interpreted by genetic codon selection, since triplet corresponds to the length of ge-netic codon. Insertion or deletion of integrate genetic codon influences the protein less slightly than the insertion or dele-tion of other types of repeats. Experimental results showed an overall amplification successful rate about 72. 9% in P. massoniana. Subsequently, 155 successfully amplified primer pairs were tested for transferability across 14 pine spe-cies and in Douglas fir. This test yielded transferability rates over 71. 0% across the 14 pine species, yet it was only 25?2% in Douglas fir. In genus Pinus, functional analyses indicated that genes with and without SSRs were significantly diverged in categories of symplast, virion and virion part classified by cellular component, in rhythmic process category classified by biological process, and in auxiliary transport protein category classified by molecular function.